Inline or to the eye of the first fly works out to fishing about the same way. Use this method if you want to fish the flies at the same level in the water column. Tie your larger/heavier fly on first and it will help carry the dropper down to the bottom. Always use tippet one size lighter to secure the second fly, so if it snags you won't lose everything.

Running off a blood/surgeon's knot tag, a tippet ring, a micro-swivel, or a dropper loop is best when you want flies to run at different levels in the water column. tie the fly you want to be ticking bottom to the main tippet, then a lighter fly to the dropper. The classic example here would be a stonefly nymph to the main tippet and a caddis pupa or soft hackle on the dropper.

You can also drop shot. Put split shot on your main tippet with the tippet melted below the shot, then run two droppers. The shot won't snag as often as the flies. This is a great method for fishing San Juan Worms out of the drift boat.